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Gene: TNFRSF4 |
Gene summary for TNFRSF4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TNFRSF4 | Gene ID | 7293 |
| Gene name | TNF receptor superfamily member 4 | |
| Gene Alias | ACT35 | |
| Cytomap | 1p36.33 | |
| Gene Type | protein-coding | GO ID | GO:0001775 | UniProtAcc | P43489 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 7293 | TNFRSF4 | LZE4T | Human | Esophagus | ESCC | 1.70e-03 | 3.36e-01 | 0.0811 |
| 7293 | TNFRSF4 | LZE7T | Human | Esophagus | ESCC | 2.56e-05 | 6.60e-01 | 0.0667 |
| 7293 | TNFRSF4 | LZE6T | Human | Esophagus | ESCC | 1.62e-02 | 4.91e-01 | 0.0845 |
| 7293 | TNFRSF4 | P74T-E | Human | Esophagus | ESCC | 1.26e-08 | 3.04e-01 | 0.1479 |
| 7293 | TNFRSF4 | P130T-E | Human | Esophagus | ESCC | 5.17e-27 | 6.94e-01 | 0.1676 |
| 7293 | TNFRSF4 | C04 | Human | Oral cavity | OSCC | 2.08e-02 | 5.12e-01 | 0.2633 |
| 7293 | TNFRSF4 | C21 | Human | Oral cavity | OSCC | 7.81e-18 | 8.34e-01 | 0.2678 |
| 7293 | TNFRSF4 | C30 | Human | Oral cavity | OSCC | 1.22e-08 | 2.43e-01 | 0.3055 |
| 7293 | TNFRSF4 | C51 | Human | Oral cavity | OSCC | 2.23e-07 | 3.70e-01 | 0.2674 |
| 7293 | TNFRSF4 | C06 | Human | Oral cavity | OSCC | 4.07e-10 | 9.70e-01 | 0.2699 |
| 7293 | TNFRSF4 | C08 | Human | Oral cavity | OSCC | 1.68e-08 | 1.80e-01 | 0.1919 |
| 7293 | TNFRSF4 | LN46 | Human | Oral cavity | OSCC | 8.10e-06 | 1.90e-01 | 0.1666 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:0016032111 | Esophagus | ESCC | viral process | 301/8552 | 415/18723 | 3.34e-29 | 1.32e-26 | 301 |
| GO:0019058111 | Esophagus | ESCC | viral life cycle | 226/8552 | 317/18723 | 1.17e-20 | 1.76e-18 | 226 |
| GO:0044403111 | Esophagus | ESCC | biological process involved in symbiotic interaction | 186/8552 | 290/18723 | 1.43e-10 | 4.16e-09 | 186 |
| GO:0051701111 | Esophagus | ESCC | biological process involved in interaction with host | 135/8552 | 203/18723 | 1.49e-09 | 3.49e-08 | 135 |
| GO:0052126111 | Esophagus | ESCC | movement in host environment | 117/8552 | 175/18723 | 1.14e-08 | 2.26e-07 | 117 |
| GO:00510908 | Esophagus | ESCC | regulation of DNA-binding transcription factor activity | 252/8552 | 440/18723 | 5.22e-07 | 6.97e-06 | 252 |
| GO:0044409111 | Esophagus | ESCC | entry into host | 96/8552 | 151/18723 | 6.73e-06 | 6.84e-05 | 96 |
| GO:003320914 | Esophagus | ESCC | tumor necrosis factor-mediated signaling pathway | 67/8552 | 99/18723 | 7.87e-06 | 7.72e-05 | 67 |
| GO:003461220 | Esophagus | ESCC | response to tumor necrosis factor | 149/8552 | 253/18723 | 1.47e-05 | 1.33e-04 | 149 |
| GO:004671827 | Esophagus | ESCC | viral entry into host cell | 89/8552 | 144/18723 | 6.84e-05 | 5.18e-04 | 89 |
| GO:007135620 | Esophagus | ESCC | cellular response to tumor necrosis factor | 132/8552 | 229/18723 | 1.69e-04 | 1.11e-03 | 132 |
| GO:004211018 | Esophagus | ESCC | T cell activation | 256/8552 | 487/18723 | 1.18e-03 | 5.87e-03 | 256 |
| GO:00434332 | Esophagus | ESCC | negative regulation of DNA-binding transcription factor activity | 103/8552 | 185/18723 | 3.86e-03 | 1.57e-02 | 103 |
| GO:001603220 | Oral cavity | OSCC | viral process | 274/7305 | 415/18723 | 2.42e-29 | 1.70e-26 | 274 |
| GO:001905820 | Oral cavity | OSCC | viral life cycle | 208/7305 | 317/18723 | 4.59e-22 | 1.00e-19 | 208 |
| GO:004440320 | Oral cavity | OSCC | biological process involved in symbiotic interaction | 173/7305 | 290/18723 | 6.80e-13 | 3.19e-11 | 173 |
| GO:005170120 | Oral cavity | OSCC | biological process involved in interaction with host | 125/7305 | 203/18723 | 5.60e-11 | 1.74e-09 | 125 |
| GO:005212620 | Oral cavity | OSCC | movement in host environment | 106/7305 | 175/18723 | 5.84e-09 | 1.26e-07 | 106 |
| GO:003461218 | Oral cavity | OSCC | response to tumor necrosis factor | 143/7305 | 253/18723 | 1.09e-08 | 2.23e-07 | 143 |
| GO:007135618 | Oral cavity | OSCC | cellular response to tumor necrosis factor | 128/7305 | 229/18723 | 1.49e-07 | 2.49e-06 | 128 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| TNFRSF4 | SNV | Missense_Mutation | novel | c.559A>C | p.Ile187Leu | p.I187L | P43489 | protein_coding | tolerated(0.14) | benign(0.001) | TCGA-DS-A1OB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
| TNFRSF4 | SNV | Missense_Mutation | rs754604681 | c.745G>A | p.Asp249Asn | p.D249N | P43489 | protein_coding | tolerated(0.74) | benign(0) | TCGA-DM-A1DA-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| TNFRSF4 | SNV | Missense_Mutation | novel | c.547N>T | p.Pro183Ser | p.P183S | P43489 | protein_coding | tolerated(0.41) | benign(0.01) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TNFRSF4 | SNV | Missense_Mutation | novel | c.14C>T | p.Ala5Val | p.A5V | P43489 | protein_coding | tolerated(0.11) | benign(0.003) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| TNFRSF4 | SNV | Missense_Mutation | rs775900244 | c.80C>T | p.Thr27Met | p.T27M | P43489 | protein_coding | deleterious(0.01) | benign(0.026) | TCGA-AX-A2HG-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TNFRSF4 | SNV | Missense_Mutation | novel | c.320G>A | p.Cys107Tyr | p.C107Y | P43489 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-B5-A11H-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Hormone Therapy | megace | SD |
| TNFRSF4 | SNV | Missense_Mutation | c.422N>T | p.Cys141Phe | p.C141F | P43489 | protein_coding | deleterious(0.03) | probably_damaging(0.966) | TCGA-MI-A75C-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| TNFRSF4 | SNV | Missense_Mutation | c.821N>A | p.Leu274Gln | p.L274Q | P43489 | protein_coding | deleterious(0) | possibly_damaging(0.887) | TCGA-UB-A7MB-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Targeted Molecular therapy | sorafenib | PD | |
| TNFRSF4 | SNV | Missense_Mutation | novel | c.316G>C | p.Val106Leu | p.V106L | P43489 | protein_coding | tolerated(0.06) | benign(0.007) | TCGA-50-5933-01 | Lung | lung adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | carboplatin | CR |
| TNFRSF4 | SNV | Missense_Mutation | c.518C>G | p.Ala173Gly | p.A173G | P43489 | protein_coding | tolerated(0.05) | possibly_damaging(0.594) | TCGA-50-7109-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| 7293 | TNFRSF4 | DRUGGABLE GENOME, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE | PF-04518600 | IVUXOLIMAB | ||
| 7293 | TNFRSF4 | DRUGGABLE GENOME, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE | 315661177 | |||
| 7293 | TNFRSF4 | DRUGGABLE GENOME, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE | antibody | 315661320 | VONLEROLIZUMAB | |
| 7293 | TNFRSF4 | DRUGGABLE GENOME, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE | GBR 830 | |||
| 7293 | TNFRSF4 | DRUGGABLE GENOME, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE | Anti-OX40 mab | |||
| 7293 | TNFRSF4 | DRUGGABLE GENOME, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE | 178101769 | |||
| 7293 | TNFRSF4 | DRUGGABLE GENOME, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE | MEDI0562 | TAVOLIMAB | ||
| 7293 | TNFRSF4 | DRUGGABLE GENOME, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE | INCAGN1949 | |||
| 7293 | TNFRSF4 | DRUGGABLE GENOME, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE | TRemelimumab + MEDI0562 |
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